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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagccgccccccaccctcaaccgaacctctgccgggtcctgatctggtcgttgcccgcgggggagctcgtcttgtgtaccgtcctgacggttttctcttctcgatgtggttgcag

Basic information

species Zea mays
transcript GRMZM2G060564_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 1
GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagccgccccccaccctcaaccgaacctctgccgggtcctgatctggtcgttgcccgcgg-gggagctcgtcttg-tgtaccgtcctgacggttttctcttctcgatgtggttgcag
|||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||||||| ||||  | || | | ||||||||||||||||||| |||| ||   |    |     | |  |     |||||| |  | || ||   |    | |||  || | ||  ||||  || ||     |||     ||| |  || ||    |  | |||||
GCGTCGTCGCAGGCCAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACCTCTGGCACTCCGATCTCACCAGCACCATCCAGGCCGACTTCCCATgtatgtcaacttttctttttcccccct----ctctgc-gaatgctaatactgcgccttcccatggcgagatttcgttctgatgggttctccctgtcgttgttgctgct----gctgatgcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211520836|gb|FL034043.1|FL034043
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|37416319|gb|CF645810.1|CF645810
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520841|gb|FL034048.1|FL034048
EST:     CAACGTCTGGCACACCGACHTGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71449020|gb|DR830070.1|DR830070
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520834|gb|FL034041.1|FL034041
EST:     CAACGTCTGGCACACCGACATGACTAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|78078643|gb|DV507055.1|DV507055
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|91048377|gb|EB158795.1|EB158795
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|50336576|gb|CO531702.1|CO531702
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGTTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|76011810|gb|DT938980.1|DT938980
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520840|gb|FL034047.1|FL034047
EST:     CAACGTCTGGMACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397639|gb|FL034039.1|FL034039
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397637|gb|FL034037.1|FL034037
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|101399172|gb|EB821460.1|EB821460
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71330287|gb|DR801905.1|DR801905
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|74234235|gb|DT642149.1|DT642149
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|26456824|gb|CA828407.1|CA828407
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|76284637|gb|DV024205.1|DV024205
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|148953515|gb|EE153023.2|EE153023
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520833|gb|FL034040.1|FL034040
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|149095487|gb|EE181140.2|EE181140
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|20512803|gb|BQ280001.1|BQ280001
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71447386|gb|DR828436.1|DR828436
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397638|gb|FL034038.1|FL034038
EST:     AACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCAMCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: AACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCC-CCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520838|gb|FL034045.1|FL034045
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|148930645|gb|EC872835.2|EC872835
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520842|gb|FL034049.1|FL034049
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|76014988|gb|DT942158.1|DT942158
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|148937865|gb|EC882083.2|EC882083
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|148949975|gb|EC895492.2|EC895492
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|74245152|gb|DT653066.1|DT653066
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|149089290|gb|EE178503.2|EE178503
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|101396680|gb|EB820265.1|EB820265
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71321160|gb|DR797280.1|DR797280
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71311330|gb|DR791989.1|DR791989
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|78107038|gb|DV525456.1|DV525456
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520837|gb|FL034044.1|FL034044
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71312763|gb|DR792909.1|DR792909
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71768464|gb|DR966401.1|DR966401
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|71315575|gb|DR794393.1|DR794393
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGT-G-G
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|50337111|gb|CO532237.1|CO532237
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGTTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 100

GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 93

GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 219

GCGTCGTCGCAGGCGAACCTCGACAAGATGCAGCTCCGCCAGAGCTACCGCAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG